2.0.0b0

What's Changed

• Add inference API and task for all BioImage.IO Model Zoo models by @qin-yu in #338

Full Changelog: 2.0.0a8...2.0.0b0

2.0.0a8

What's Changed since v2.0.0a2

GUI improvements

• New export widget by @lorenzocerrone in #341
• Proofreading improvements by @lorenzocerrone in #355
• Add image pair operation widget/task/functionals/docs by @qin-yu in #370

CLI (Headless) improvement

• Improved Headless + gui by @lorenzocerrone in #356
• fix: allow more runtime errors in find_batch_size() by @qin-yu in #359
• fix: allow but warn all runtime errors in 3D find_a_max_patch_shape() by @qin-yu in #361

Functionality bug fixes

• Fix voxel size unit by @qin-yu in #343
• fix: #353 foreground fix now work in 2D by @lorenzocerrone in #354
• fix: widgets should have optional arg for updating other widgets by @qin-yu in #362
• Fix smart load | Make extension check case-insensitive by @qin-yu in #368

Compatibility and installation

• Fix perfomance on mac by @lorenzocerrone in #337
• fix (#344): update windows install instructions by @lorenzocerrone in #347
• Match conda recipe and include package_data logo by @qin-yu in #348
• fix(env): Pydantic v2.10 causes bioimageio.spec issues by @qin-yu in #363

CI/CD

• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #349
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #357
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #369

Docs

• Fix and promote PlantSeg v1 installation by @qin-yu in #364
• ci(docs): fetch all git history/tags/branches for MkDocs dates by @qin-yu in #366

Full Changelog: 2.0.0a2...2.0.0a8

2.0.0a7

What's Changed

• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #357
• fix: allow more runtime errors in find_batch_size() by @qin-yu in #359
• fix: allow but warn all runtime errors in 3D find_a_max_patch_shape() by @qin-yu in #361
• fix: widgets should have optional arg for updating other widgets by @qin-yu in #362

Full Changelog: 2.0.0a5...2.0.0a7

2.0.0a5

What's Changed

• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #349
• fix: #353 by @lorenzocerrone in #354
• Proofreading improvements by @lorenzocerrone in #355
• Improved Headless + gui by @lorenzocerrone in #356

Full Changelog: 2.0.0a4...2.0.0a5

2.0.0a4

What's Changed

• fix (#344): update windows install instructions by @lorenzocerrone in #347
• Match conda recipe and include package_data logo by @qin-yu in #348

Full Changelog: 2.0.0a3...2.0.0a4

2.0.0a3

What's Changed

• New export widget by @lorenzocerrone in #341
• Fix perfomance on mac by @lorenzocerrone in #337
• Fix voxel size unit by @qin-yu in #343

Full Changelog: 2.0.0a2...2.0.0a3

2.0.0a2

What's Changed since v1.8.0

Features

• feat(pred): check and free VRAM for prediction with oversized patch by @qin-yu in #272
• Automatic patch shape recommendation by @qin-yu in #302
• Compute best patch and halo shapes by default, reduce user effort by @qin-yu in #307
  • Fix size finder and widgets for 2D UNet by @qin-yu in #313
• Add un-/re-do and save-/load-states for proofreading tool by @qin-yu in #323

Infrastructure & GUI

and recover after infra refactor

• Unify and standardise logging in PlantSeg v2 by @qin-yu in #296
• Add important widgets and improve logger further by @qin-yu in #297
• PlantSeg.Core: ModelZoo, PlantSegImage, and VoxelSize by @qin-yu in #298
• Tests: Fix all existing tests by @qin-yu in #299
• Test and refactor .core and functionals.dataprocessing by @qin-yu in #303
• Properly refresh ComboBox choices with functions by @qin-yu in #305
• Make VoxelSize iterable and array-like, remove .is_valid by @qin-yu in #310
• refactor: use magicgui.types.Separator by @qin-yu in #311
• Improve model filters | Use RadioButtons | Custom modality by @qin-yu in #314
• Group widgets for batch .hide()/.show() by @qin-yu in #317
• Fix and integrate lifted multicut widget into agglomeration widget by @qin-yu in #328
• Refactor and recover widgets: cropping and label processing by @qin-yu in #330
• PlantSeg v2: Final polishment of GUI by @qin-yu in #326
• refactor(GUI): rename and reorder widgets for intuitive sequential flow by @qin-yu in #331
• PlantSeg v2: full codebase refactor with unified task framework, enhanced prediction/proofreading, and metadata handling by @lorenzocerrone in #285

Bug fixes

• fix(cropping): use RangeSlider to fix #278 | handle None image by @qin-yu in #279
• fix(widget-IO): temp fix #282 and auto generate layer name by @qin-yu in #304
• Fix TIFF default layer name and hide key widget by @qin-yu in #312
• Fix and document distance transform watershed for 2D pmaps/images by @qin-yu in #318
• fix h5 export by @lorenzocerrone in #335
• fix: avoid reading logo file from docs folder by @qin-yu in #336

CI/CD

• Use pre-commit by @qin-yu in #263
• chore: migrate from bumpversion to bump-my-version by @qin-yu in #266
• chore(pre-commit): add conventional commits by @qin-yu in #267
• fix(installation): remove old configs if KeyError | macOS installation by @qin-yu in #277
• fixes PlantSeg crash on apple silicon #273 by @lorenzocerrone in #275
• Use Codecov by @qin-yu in #300
• Fix version related issues: bump version, comparison and Anaconda upload by @qin-yu in #333

Docs

• fix: links in docs, docstring warning and theme override by @qin-yu in #269
• fix(docs): teach Qt to find napari icons by @qin-yu in #271
• PlantSeg v2 docs base by @qin-yu in #320
• Recover and document over-/under-seg fix by nuclei by @qin-yu in #321
• PlantSeg v2: Finalise docs by @qin-yu in #322
• Record issue missing button by @qin-yu in #327

New Contributors

• @pre-commit-ci made their first contribution in #265

Full Changelog: 1.8.0...2.0.0-alpha

1.8.0

What's Changed

• 🏠 PlantSeg was moved to https://github.com/kreshuklab/plant-seg/

Features

• 🦒 Execute PlantSeg-compatible models in 🦒 BioImage.IO Model Zoo 🐿️ by @qin-yu in #247 & #248
• 📏 Refactor rescaling widget | Rearrange widgets by @lorenzocerrone in #249
  • Improve use of Enum as widget choices and fix types by @qin-yu in #256
• 🤖 Recommend users a halo for U-Nets by @qin-yu in #252

Documentation

• Doc: Data/models, train/add new models, Jupyter Book remnant by @qin-yu in #240
• Doc: API and screenshots by @lorenzocerrone in #249
  • Doc: Fix docs build in CI by @lorenzocerrone in #257
  • Doc: Fix and update rescaling widget screenshot docs by @qin-yu in #259
• Doc: Add revision date and committer plugins by @qin-yu in #260

Tests

• Tests for rescaling widget by @qin-yu in #258

Bug Fix

• Type Fix: np.array is not a type, change to np.ndarray by @qin-yu in #231
• Fix Legacy GUI after v1.7.0 by @qin-yu in #237
• Fix CYX/CZYX pad/halo, fix io.zarr/tests, fix typing, refactor model load by @qin-yu in #233
• Headless: Handle multi-channel prediction output and add docs by @qin-yu in #239
• Test Fix: always-skipped test and misleading name by @qin-yu in #262

Full Changelog: 1.7.0...1.8.0

1.7.0

What's Changed

• 🥳 PlantSeg is on conda-forge as plant-seg at anaconda.org/conda-forge/plant-seg
• 📖 PlantSeg documentation is published at hci-unihd.github.io/plant-seg/

Bug Fix

• Fix multi-channel output layers in Napari by @qin-yu in #184
• Fix halo implementation and tiling artefact by @qin-yu in #220 & #223
• Fix voxel size precision and font size in Napari GUI by @qin-yu in #227

Features

• New key & channel selection for all interfaces by @qin-yu @lorenzocerrone in #165, #184 & #212
• Add option to set home_path via PLANTSEG_HOME env-variable. by @tibuch in #170
• Add support for training by @wolny in #159
• Add Lifted MultiCut in GUI by @qin-yu in #184
• Add option to only run official models in "Try all Available Models" by @qin-yu in #207
• Add widget: remove objects using a probability map by @qin-yu in #202
• Add validation, adaptation and halo to prediction widgets by @qin-yu in #211
• Add widget managers and rearrange tabs by @lorenzocerrone @qin-yu in #221 & #227

Models

• Ensure compatibility with models trained with pytorch-3dunet by @wolny in #160
• Add a generic nuclear model for GoNuclear paper by @qin-yu in #169 & #193
• Central model records by @qin-yu in #216

Documentation

• Improve docs and create website at https://hci-unihd.github.io/plant-seg/ by @qin-yu in #179, #191, #229 & #230
• Update mamba install by @jackyko1991 in #180

Full Changelog: 1.6.0...1.7.0

New Maintainer

• @qin-yu became a maintainer

New Contributors

• @qin-yu made their first contribution in #165
• @tibuch made their first contribution in #170
• @jackyko1991 made their first contribution in #180

Overall improvements and bug fixes

What's Changed

• Move models to zenodo by @wolny in #135
• Improved proofreading by @lorenzocerrone in #132
• Fix incorrect model weights on Zenodo by @wolny in #139
• Minor UI improvements by @lorenzocerrone in #137
• Remove pytorch-3dunet dependency by @wolny in #141
• Improve batch_size selection by @wolny in #147
• Better models names by @lorenzocerrone in #148
• Add nice widgets callbacks by @lorenzocerrone in #149
• Read write zarrs by @Mohinta2892 in #150
• Add zarr support by @lorenzocerrone in #151

New Contributors

• @Mohinta2892 made their first contribution in #150

Full Changelog: 1.5.2...1.6.0